[gmx-users] free energy

Nilesh Dhumal ndhumal at andrew.cmu.edu
Mon Jan 11 01:02:45 CET 2010


Thanks Justin,
I am not setting any Lennard-Jones parameters to zero for  part B. I put 
zero charge on all atoms for Part B. (Lennard Jones parameters for B are
same as Part A).

I am using default parameters for  "couple-lambda0" and "couple-lambda1".
For one of my simulation (glucose + ionic liquids) I am getting solvation
free energy 35.5 Kcal/mol.
Is it too high?

Nilesh

On Sun, January 10, 2010 1:08 pm, Justin A. Lemkul wrote:
>

>
> On 1/10/10 1:03 PM, Nilesh Dhumal wrote:
>
>> Hello Justin,
>> Should I add dum_opls no. in atom type file in which Lennard-jones
>> parameters will set to zero. OR.
>> I don't have to modify anything prog.will take care of lennard-jones
>> interactions. I have put charge zero on all atom in TYPE B.
>>
>
> You shouldn't have to do make any modifications to the topology
> whatsoever, according to the documentation.  The "couple-lambda0" and
> "couple-lambda1"
> parameters should do the decoupling for you.
>
> -Justin
>
>
>> Nilesh
>>
>>
>> On Sun, January 3, 2010 12:57 pm, Justin A. Lemkul wrote:
>>
>>>
>>
>>>
>>> Nilesh Dhumal wrote:
>>>
>>>
>>>> THanks Justin.
>>>> I am using Groamcs 4.0.7 version. I will do more simulation with
>>>> more lambada value betwen 0 to 0.1.
>>>
>>> I really think this is less significant than point #1 I mentioned
>>> before. Be
>>> sure you are actually setting the relevant .mdp parameters
>>> (couple-lambda0,
>>> couple-lambda1, etc) as they will heavily influence the results.
>>> Leaving
>>> them as default (as you are doing, per the .mdp file you provided) may
>>>  give you something other than what you want.
>>>
>>> And do consult the links I provided; they give excellent background
>>> on the nature of these calculations.
>>>
>>> -Justin
>>>
>>>
>>>
>>>> Thanks.
>>>> Nilesh
>>>>
>>>>
>>>>
>>>> On Sun, January 3, 2010 12:39 pm, Justin A. Lemkul wrote:
>>>>
>>>>
>>>>
>>>>> Nilesh Dhumal wrote:
>>>>>
>>>>>
>>>>>
>>>>>> Hey All,
>>>>>> I am trying to calculate the solvation free energy of glucose in
>>>>>>  ionic liquids. I am getting really large  value for lamda=0 in
>>>>>>  vacuum and solvent as well. I am getting final solvation
>>>>>> energy value ~ 310 kJ/mol. Can you tell me where I am   wrong.
>>>>>>
>>>>> There are several possibilities:
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> 1. Are you decoupling LJ and Coulombic interactions
>>>>> simultaneously? They
>>>>> should be done in separate steps, or else you get very large
>>>>> errors.
>>>>>
>>>>> 2. You probably need a lot more lambda points to properly define
>>>>> the curve.  For strongly hydrogen-bonding solutes, you should
>>>>> probably include closely-spaced points near lambda = 0 (the
>>>>> fully-coupled state), like 0.005, 0.01, 0.015, etc. The curve from
>>>>> 0 to 0.1 will otherwise be ill-defined and prone to large errors.
>>>>>
>>>>> You also do not say which version of the code you are using.  The
>>>>>  free energy code has been tweaked in version 4.0 such that
>>>>> topology handling is different, and the procedure is actually
>>>>> quite a bit more streamlined, given the .mdp options.
>>>>>
>>>>> Might I recommend:
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> http://www.alchemistry.org/wiki/index.php/Best_Practices
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> http://md.chem.rug.nl/education/Free-Energy_Course/index.html
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> -Justin
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>> Here I have pasted the the lamda value in vacuum and  solvent
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Vacuum 		 Solvent
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> 0.0 527.16	0.0 4284.769
>>>>>> 0.1 74.119	0.1 161.606
>>>>>> 0.2 37.9665	0.2 -16.3176
>>>>>> 0.3 28.748	0.3 -52.488
>>>>>> 0.4 7.555	0.4 -4.3341
>>>>>> 0.5 1.495	0.5 6.996
>>>>>> 0.6 -4.796	0.6 155.485
>>>>>> 0.7 2.361	0.7 174.20
>>>>>> 0.8 3.69	0.8 193.016
>>>>>> 0.9 5.483	0.9  201.820
>>>>>> 0.92 6.391	0.92 211.79
>>>>>> 1.0 8.887	1.0  227.79
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> For each lamda value I equibrate the system for 1ns and run the
>>>>>>  dynamics for 4 ns. here is dynamics file I used. pasted the
>>>>>> topology file at the end.
>>>>>>
>>>>>>
>>>>>> title               =  cpeptide MD cpp                 =
>>>>>> /usr/bin/cpp
>>>>>> constraints         =  none integrator          =  md dt =
>>>>>> 0.001
>>>>>> ; ps !
>>>>>> nsteps              =  4000000     ; total 5 ps. nstcomm =  1
>>>>>> nstxout             =  50 nstvout             =  0 nstfout =
>>>>>> 0
>>>>>> nstlist             =  10 ns_type             =  grid rlist =
>>>>>> 1.0
>>>>>> rcoulomb            =  1.0 rvdw                =  1.4
>>>>>> coulombtype = PME
>>>>>> vdwtype             = cut-off pbc                 = xyz
>>>>>> fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz =
>>>>>> 0 pme_order           = 4 ewald_rtol          = 1e-5
>>>>>> optimize_fft        = yes ; Berendsen temperature coupling is on
>>>>>> Tcoupl = v-rescale tau_t = 0.1 tc-grps
>>>>>> =system ref_t =   350 ; Pressure coupling is  on
>>>>>> Pcoupl              = parrinello-rahman
>>>>>> pcoupltype          = isotropic tau_p               =  0.5
>>>>>> compressibility =  4.5e-5 ref_p               =  1.0 ; Generate
>>>>>> velocites is on at 300 K. gen_vel             =  yes gen_temp
>>>>>> =  350.0 gen_seed =
>>>>>> 173529
>>>>>> free_energy         = yes init_lambda         = 0.00 sc-alpha =
>>>>>> 0.6
>>>>>> sc_power            = 1
>>>>>>
>>>>>>
>>>>>> Thanks
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Nilesh
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Topology file (not pasted whole because of size)
>>>>>> ;
>>>>>> ;	File 'glu-ac.top' was generated
>>>>>> ;	By user: ndhumal (36026)
>>>>>> ;	On host: c20
>>>>>> ;	At date: Tue Dec 15 15:25:07 2009
>>>>>> ;
>>>>>> ;	This is your topology file
>>>>>> ;	Gromacs Runs One Microsecond At Cannonball Speeds
>>>>>> ;
>>>>>> ; Include forcefield parameters
>>>>>> #include "ffoplsaa.itp"
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> [ moleculetype ]
>>>>>> ; Name            nrexcl
>>>>>> Protein             3
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> [ atoms ]
>>>>>> ;   nr       type  resnr residue  atom   cgnr     charge
>>>>>> mass typeB chargeB      massB 1   opls_180      1    GUL      O
>>>>>> 1
>>>>>> -0.4    15.9994
>>>>>> opls_180  0.0    15.9994 2   opls_159      1    GUL     C2
>>>>>> 2
>>>>>> 0.365     12.011
>>>>>> opls_159  0.0     12.011 3   opls_159      1    GUL     C3
>>>>>> 2
>>>>>> 0.205     12.011
>>>>>> opls_159  0.0     12.011 4   opls_159      1    GUL     C4
>>>>>> 2
>>>>>> 0.205     12.011
>>>>>> opls_159  0.0     12.011 5   opls_159      1    GUL     C5
>>>>>> 2
>>>>>> 0.205     12.011
>>>>>> opls_159  0.0     12.011 6   opls_137      1    GUL     C6
>>>>>> 2
>>>>>> 0.17     12.011
>>>>>> opls_137  0.0     12.011 7   opls_159      1    GUL     C7
>>>>>> 2
>>>>>> 0.145     12.011
>>>>>> opls_159  0.0     12.011 8   opls_169      1    GUL     O8
>>>>>> 3
>>>>>> -0.7    15.9994
>>>>>> opls_169  0.0    15.9994 9   opls_169      1    GUL     O9
>>>>>> 3
>>>>>> -0.7    15.9994
>>>>>> opls_169  0.0    15.9994 10   opls_169      1    GUL    O10
>>>>>> 3
>>>>>> -0.7    15.9994
>>>>>> opls_169  0.0    15.9994 11   opls_169      1    GUL    O11
>>>>>> 3
>>>>>> -0.7    15.9994
>>>>>> opls_169  0.0    15.9994 12   opls_154      1    GUL    O12
>>>>>> 3
>>>>>> -0.683    15.9994
>>>>>> opls_154  0.0    15.9994 13   opls_140      1    GUL    H13
>>>>>> 4
>>>>>> 0.1      1.008
>>>>>> opls_140  0.0      1.008 14   opls_140      1    GUL    H14
>>>>>> 4
>>>>>> 0.06      1.008
>>>>>> opls_140  0.0      1.008 15   opls_140      1    GUL    H15
>>>>>> 4
>>>>>> 0.06      1.008
>>>>>> opls_140  0.0      1.008 16   opls_140      1    GUL    H16
>>>>>> 4
>>>>>> 0.06      1.008
>>>>>> opls_140  0.0      1.008 17   opls_140      1    GUL    H17
>>>>>> 4
>>>>>> 0.03      1.008
>>>>>> opls_140  0.0      1.008 18   opls_155      1    GUL    H18
>>>>>> 5
>>>>>> 0.435      1.008
>>>>>> opls_155  0.0      1.008 19   opls_155      1    GUL    H19
>>>>>> 5
>>>>>> 0.435      1.008
>>>>>> opls_155  0.0      1.008 20   opls_155      1    GUL    H20
>>>>>> 5
>>>>>> 0.435      1.008
>>>>>> opls_155  0.0      1.008 21   opls_155      1    GUL    H21
>>>>>> 5
>>>>>> 0.435      1.008
>>>>>> opls_155  0.0      1.008 22   opls_140      1    GUL    H22
>>>>>> 5
>>>>>> 0.06      1.008
>>>>>> opls_140  0.0      1.008 23   opls_140      1    GUL    H23
>>>>>> 5
>>>>>> 0.06      1.008
>>>>>> opls_140  0.0      1.008 24   opls_155      1    GUL    H24
>>>>>> 6
>>>>>> 0.418      1.008
>>>>>> opls_155  0.0      1.008 25   opls_561      2    EMI      C
>>>>>> 7
>>>>>> -0.13     12.011   ;
>>>>>> qtot -0.13 26   opls_561      2    EMI     C2      8      -0.13
>>>>>> 12.011   ;
>>>>>> qtot -0.26 27   opls_557      2    EMI     N3      9       0.15
>>>>>> 14.0067   ;
>>>>>> qtot -0.11 28   opls_558      2    EMI     C4     10      -0.11
>>>>>> 12.011   ;
>>>>>> qtot -0.22 29   opls_557      2    EMI     N5     11       0.15
>>>>>> 14.0067   ;
>>>>>> qtot -0.07 30   opls_135      2    EMI     C6     12      -0.17
>>>>>> 12.011   ;
>>>>>> qtot -0.24 31   opls_136      2    EMI     C7     13      -0.05
>>>>>> 12.011   ;
>>>>>> qtot -0.29 32   opls_135      2    EMI     C8     14      -0.17
>>>>>> 12.011   ;
>>>>>> qtot -0.46 33   opls_564      2    EMI     H9     15       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot -0.25 34   opls_564      2    EMI    H10     15       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot -0.04 35   opls_563      2    EMI    H11     15       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 0.17 36   opls_140      2    EMI    H12     16       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 0.3 37   opls_140      2    EMI    H13     16       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 0.43 38   opls_140      2    EMI    H14     16       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 0.56 39   opls_140      2    EMI    H15     17       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 0.69 40   opls_140      2    EMI    H16     17       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 0.82 41   opls_140      2    EMI    H17     18       0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 0.88 42   opls_140      2    EMI    H18     18       0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 0.94 43   opls_140      2    EMI    H19     18       0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 1 44   opls_561      3    EMI      C     19      -0.13
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 0.87 45   opls_561      3    EMI     C2     20      -0.13
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 0.74 46   opls_557      3    EMI     N3     21       0.15
>>>>>> 14.0067
>>>>>> ;
>>>>>> qtot 0.89 47   opls_558      3    EMI     C4     22      -0.11
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 0.78 48   opls_557      3    EMI     N5     23       0.15
>>>>>> 14.0067
>>>>>> ;
>>>>>> qtot 0.93 49   opls_135      3    EMI     C6     24      -0.17
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 0.76 50   opls_136      3    EMI     C7     25      -0.05
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 0.71 51   opls_135      3    EMI     C8     26      -0.17
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 0.54 52   opls_564      3    EMI     H9     27       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 0.75 53   opls_564      3    EMI    H10     27       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 0.96 54   opls_563      3    EMI    H11     27       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 1.17 55   opls_140      3    EMI    H12     28       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 1.3 56   opls_140      3    EMI    H13     28       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 1.43 57   opls_140      3    EMI    H14     28       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 1.56 58   opls_140      3    EMI    H15     29       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 1.69 59   opls_140      3    EMI    H16     29       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 1.82 60   opls_140      3    EMI    H17     30       0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 1.88 61   opls_140      3    EMI    H18     30       0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 1.94 62   opls_140      3    EMI    H19     30       0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 2 63   opls_561      4    EMI      C     31      -0.13
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 1.87 64   opls_561      4    EMI     C2     32      -0.13
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 1.74 65   opls_557      4    EMI     N3     33       0.15
>>>>>> 14.0067
>>>>>> ;
>>>>>> qtot 1.89 66   opls_558      4    EMI     C4     34      -0.11
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 1.78 67   opls_557      4    EMI     N5     35       0.15
>>>>>> 14.0067
>>>>>> ;
>>>>>> qtot 1.93 68   opls_135      4    EMI     C6     36      -0.17
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 1.76 69   opls_136      4    EMI     C7     37      -0.05
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 1.71 70   opls_135      4    EMI     C8     38      -0.17
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 1.54 71   opls_564      4    EMI     H9     39       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 1.75 72   opls_564      4    EMI    H10     39       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 1.96 73   opls_563      4    EMI    H11     39       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 2.17 74   opls_140      4    EMI    H12     40       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 2.3 75   opls_140      4    EMI    H13     40       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 2.43 76   opls_140      4    EMI    H14     40       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 2.56 77   opls_140      4    EMI    H15     41       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 2.69 78   opls_140      4    EMI    H16     41       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 2.82 79   opls_140      4    EMI    H17     42       0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 2.88 80   opls_140      4    EMI    H18     42       0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 2.94 81   opls_140      4    EMI    H19     42       0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 3 82   opls_561      5    EMI      C     43      -0.13
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 2.87 83   opls_561      5    EMI     C2     44      -0.13
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 2.74 84   opls_557      5    EMI     N3     45       0.15
>>>>>> 14.0067
>>>>>> ;
>>>>>> qtot 2.89 85   opls_558      5    EMI     C4     46      -0.11
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 2.78 86   opls_557      5    EMI     N5     47       0.15
>>>>>> 14.0067
>>>>>> ;
>>>>>> qtot 2.93 87   opls_135      5    EMI     C6     48      -0.17
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 2.76 88   opls_136      5    EMI     C7     49      -0.05
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 2.71 89   opls_135      5    EMI     C8     50      -0.17
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 2.54 90   opls_564      5    EMI     H9     51       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 2.75 91   opls_564      5    EMI    H10     51       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 2.96 92   opls_563      5    EMI    H11     51       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 3.17 93   opls_140      5    EMI    H12     52       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 3.3 94   opls_140      5    EMI    H13     52       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 3.43 95   opls_140      5    EMI    H14     52       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 3.56 96   opls_140      5    EMI    H15     53       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 3.69 97   opls_140      5    EMI    H16     53       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 3.82 98   opls_140      5    EMI    H17     54       0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 3.88 99   opls_140      5    EMI    H18     54       0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 3.94 100   opls_140      5    EMI    H19     54       0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 4 101   opls_561      6    EMI      C     55      -0.13
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 3.87 102   opls_561      6    EMI     C2     56      -0.13
>>>>>> 12.011   ;
>>>>>> qtot 3.74 103   opls_557      6    EMI     N3     57       0.15
>>>>>> 14.0067   ;
>>>>>> qtot 3.89 104   opls_558      6    EMI     C4     58      -0.11
>>>>>> 12.011   ;
>>>>>> qtot 3.78 105   opls_557      6    EMI     N5     59       0.15
>>>>>> 14.0067   ;
>>>>>> qtot 3.93 106   opls_135      6    EMI     C6     60      -0.17
>>>>>> 12.011   ;
>>>>>> qtot 3.76 107   opls_136      6    EMI     C7     61      -0.05
>>>>>> 12.011   ;
>>>>>> qtot 3.71 108   opls_135      6    EMI     C8     62      -0.17
>>>>>> 12.011   ;
>>>>>> qtot 3.54 109   opls_564      6    EMI     H9     63       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 3.75 110   opls_564      6    EMI    H10     63       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 3.96 111   opls_563      6    EMI    H11     63       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 4.17 112   opls_140      6    EMI    H12     64       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 4.3 113   opls_140      6    EMI    H13     64       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 4.43 114   opls_140      6    EMI    H14     64       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 4.56 115   opls_140      6    EMI    H15     65       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 4.69 116   opls_140      6    EMI    H16     65       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 4.82 117   opls_140      6    EMI    H17     66       0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 4.88 118   opls_140      6    EMI    H18     66       0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 4.94 119   opls_140      6    EMI    H19     66       0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 5 120   opls_561      7    EMI      C     67      -0.13
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 4.87 121   opls_561      7    EMI     C2     68      -0.13
>>>>>> 12.011   ;
>>>>>> qtot 4.74 122   opls_557      7    EMI     N3     69       0.15
>>>>>> 14.0067   ;
>>>>>> qtot 4.89 123   opls_558      7    EMI     C4     70      -0.11
>>>>>> 12.011   ;
>>>>>> qtot 4.78 124   opls_557      7    EMI     N5     71       0.15
>>>>>> 14.0067   ;
>>>>>> qtot 4.93 125   opls_135      7    EMI     C6     72      -0.17
>>>>>> 12.011   ;
>>>>>> qtot 4.76 126   opls_136      7    EMI     C7     73      -0.05
>>>>>> 12.011   ;
>>>>>> qtot 4.71 127   opls_135      7    EMI     C8     74      -0.17
>>>>>> 12.011   ;
>>>>>> qtot 4.54 128   opls_564      7    EMI     H9     75       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 4.75 129   opls_564      7    EMI    H10     75       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 4.96 130   opls_563      7    EMI    H11     75       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 5.17 131   opls_140      7    EMI    H12     76       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 5.3 132   opls_140      7    EMI    H13     76       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 5.43 133   opls_140      7    EMI    H14     76       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 5.56 134   opls_140      7    EMI    H15     77       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 5.69 135   opls_140      7    EMI    H16     77       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 5.82 136   opls_140      7    EMI    H17     78       0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 5.88 137   opls_140      7    EMI    H18     78       0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 5.94 138   opls_140      7    EMI    H19     78       0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 6 139   opls_561      8    EMI      C     79      -0.13
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 5.87 140   opls_561      8    EMI     C2     80      -0.13
>>>>>> 12.011   ;
>>>>>> qtot 5.74 141   opls_557      8    EMI     N3     81       0.15
>>>>>> 14.0067   ;
>>>>>> qtot 5.89 142   opls_558      8    EMI     C4     82      -0.11
>>>>>> 12.011   ;
>>>>>> qtot 5.78 143   opls_557      8    EMI     N5     83       0.15
>>>>>> 14.0067   ;
>>>>>> qtot 5.93 144   opls_135      8    EMI     C6     84      -0.17
>>>>>> 12.011   ;
>>>>>> qtot 5.76 145   opls_136      8    EMI     C7     85      -0.05
>>>>>> 12.011   ;
>>>>>> qtot 5.71 146   opls_135      8    EMI     C8     86      -0.17
>>>>>> 12.011   ;
>>>>>> qtot 5.54 147   opls_564      8    EMI     H9     87       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 5.75 148   opls_564      8    EMI    H10     87       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 5.96 149   opls_563      8    EMI    H11     87       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 6.17 150   opls_140      8    EMI    H12     88       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 6.3 151   opls_140      8    EMI    H13     88       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 6.43 152   opls_140      8    EMI    H14     88       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 6.56 153   opls_140      8    EMI    H15     89       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 6.69 154   opls_140      8    EMI    H16     89       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 6.82 155   opls_140      8    EMI    H17     90       0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 6.88 156   opls_140      8    EMI    H18     90       0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 6.94 157   opls_140      8    EMI    H19     90       0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 7 158   opls_561      9    EMI      C     91      -0.13
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 6.87 159   opls_561      9    EMI     C2     92      -0.13
>>>>>> 12.011   ;
>>>>>> qtot 6.74 160   opls_557      9    EMI     N3     93       0.15
>>>>>> 14.0067   ;
>>>>>> qtot 6.89 161   opls_558      9    EMI     C4     94      -0.11
>>>>>> 12.011   ;
>>>>>> qtot 6.78 162   opls_557      9    EMI     N5     95       0.15
>>>>>> 14.0067   ;
>>>>>> qtot 6.93 163   opls_135      9    EMI     C6     96      -0.17
>>>>>> 12.011   ;
>>>>>> qtot 6.76 164   opls_136      9    EMI     C7     97      -0.05
>>>>>> 12.011   ;
>>>>>> qtot 6.71 165   opls_135      9    EMI     C8     98      -0.17
>>>>>> 12.011   ;
>>>>>> qtot 6.54 166   opls_564      9    EMI     H9     99       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 6.75 167   opls_564      9    EMI    H10     99       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 6.96 168   opls_563      9    EMI    H11     99       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 7.17 169   opls_140      9    EMI    H12    100       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 7.3 170   opls_140      9    EMI    H13    100       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 7.43 171   opls_140      9    EMI    H14    100       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 7.56 172   opls_140      9    EMI    H15    101       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 7.69 173   opls_140      9    EMI    H16    101       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 7.82 174   opls_140      9    EMI    H17    102       0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 7.88 175   opls_140      9    EMI    H18    102       0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 7.94 176   opls_140      9    EMI    H19    102       0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 8 177   opls_561     10    EMI      C    103      -0.13
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 7.87 178   opls_561     10    EMI     C2    104      -0.13
>>>>>> 12.011   ;
>>>>>> qtot 7.74 179   opls_557     10    EMI     N3    105       0.15
>>>>>> 14.0067   ;
>>>>>> qtot 7.89 180   opls_558     10    EMI     C4    106      -0.11
>>>>>> 12.011   ;
>>>>>> qtot 7.78 181   opls_557     10    EMI     N5    107       0.15
>>>>>> 14.0067   ;
>>>>>> qtot 7.93 182   opls_135     10    EMI     C6    108      -0.17
>>>>>> 12.011   ;
>>>>>> qtot 7.76 183   opls_136     10    EMI     C7    109      -0.05
>>>>>> 12.011   ;
>>>>>> qtot 7.71 184   opls_135     10    EMI     C8    110      -0.17
>>>>>> 12.011   ;
>>>>>> qtot 7.54 185   opls_564     10    EMI     H9    111       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 7.75 186   opls_564     10    EMI    H10    111       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 7.96 187   opls_563     10    EMI    H11    111       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 8.17 188   opls_140     10    EMI    H12    112       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 8.3 189   opls_140     10    EMI    H13    112       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 8.43 190   opls_140     10    EMI    H14    112       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 8.56 191   opls_140     10    EMI    H15    113       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 8.69 192   opls_140     10    EMI    H16    113       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 8.82 193   opls_140     10    EMI    H17    114       0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 8.88 194   opls_140     10    EMI    H18    114       0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 8.94 195   opls_140     10    EMI    H19    114       0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 9 196   opls_561     11    EMI      C    115      -0.13
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 8.87 197   opls_561     11    EMI     C2    116      -0.13
>>>>>> 12.011   ;
>>>>>> qtot 8.74 198   opls_557     11    EMI     N3    117       0.15
>>>>>> 14.0067   ;
>>>>>> qtot 8.89 199   opls_558     11    EMI     C4    118      -0.11
>>>>>> 12.011   ;
>>>>>> qtot 8.78 200   opls_557     11    EMI     N5    119       0.15
>>>>>> 14.0067   ;
>>>>>> qtot 8.93 201   opls_135     11    EMI     C6    120      -0.17
>>>>>> 12.011   ;
>>>>>> qtot 8.76 202   opls_136     11    EMI     C7    121      -0.05
>>>>>> 12.011   ;
>>>>>> qtot 8.71 203   opls_135     11    EMI     C8    122      -0.17
>>>>>> 12.011   ;
>>>>>> qtot 8.54 204   opls_564     11    EMI     H9    123       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 8.75 205   opls_564     11    EMI    H10    123       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 8.96 206   opls_563     11    EMI    H11    123       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 9.17 207   opls_140     11    EMI    H12    124       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 9.3 208   opls_140     11    EMI    H13    124       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 9.43 209   opls_140     11    EMI    H14    124       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 9.56 210   opls_140     11    EMI    H15    125       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 9.69 211   opls_140     11    EMI    H16    125       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 9.82 212   opls_140     11    EMI    H17    126       0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 9.88 213   opls_140     11    EMI    H18    126       0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 9.94 214   opls_140     11    EMI    H19    126       0.06
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 10 215   opls_561     12    EMI      C    127      -0.13
>>>>>> 12.011
>>>>>> ;
>>>>>> qtot 9.87 216   opls_561     12    EMI     C2    128      -0.13
>>>>>> 12.011   ;
>>>>>> qtot 9.74 217   opls_557     12    EMI     N3    129       0.15
>>>>>> 14.0067   ;
>>>>>> qtot 9.89 218   opls_558     12    EMI     C4    130      -0.11
>>>>>> 12.011   ;
>>>>>> qtot 9.78 219   opls_557     12    EMI     N5    131       0.15
>>>>>> 14.0067   ;
>>>>>> qtot 9.93 220   opls_135     12    EMI     C6    132      -0.17
>>>>>> 12.011   ;
>>>>>> qtot 9.76 221   opls_136     12    EMI     C7    133      -0.05
>>>>>> 12.011   ;
>>>>>> qtot 9.71 222   opls_135     12    EMI     C8    134      -0.17
>>>>>> 12.011   ;
>>>>>> qtot 9.54 223   opls_564     12    EMI     H9    135       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 9.75 224   opls_564     12    EMI    H10    135       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 9.96 225   opls_563     12    EMI    H11    135       0.21
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 10.17 226   opls_140     12    EMI    H12    136       0.13
>>>>>>  1.008   ;
>>>>>> qtot 10.3 227   opls_140     12    EMI    H13    136       0.13
>>>>>> 1.008
>>>>>> ;
>>>>>> qtot 10.43 228   opls_140     12    EMI    H14    136       0.13
>>>>>>  1.008   ;
>>>>>> qtot 10.56 229   opls_140     12    EMI    H15    137       0.13
>>>>>>  1.008   ;
>>>>>> qtot 10.69 230   opls_140     12    EMI    H16    137       0.13
>>>>>>  1.008   ;
>>>>>> qtot 10.82 231   opls_140     12    EMI    H17    138       0.06
>>>>>>  1.008   ;
>>>>>> qtot 10.88 232   opls_140     12    EMI    H18    138       0.06
>>>>>>  1.008   ;
>>>>>> qtot 10.94 233   opls_140     12    EMI    H19    138       0.06
>>>>>>  1.008   ;
>>>>>> qtot 11
>>>>>>
>>>>> --
>>>>> ========================================
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Justin A. Lemkul
>>>>> Ph.D. Candidate
>>>>> ICTAS Doctoral Scholar
>>>>> MILES-IGERT Trainee
>>>>> Department of Biochemistry
>>>>> Virginia Tech
>>>>> Blacksburg, VA
>>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ========================================
>>>>> --
>>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>> Please search the archive at http://www.gromacs.org/search before
>>>>> posting! Please don't post (un)subscribe requests to the list. Use
>>>>> the www interface or send it to gmx-users-request at gromacs.org.
>>>>> Can't
>>>>> post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>
>>> --
>>> ========================================
>>>
>>>
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> MILES-IGERT Trainee
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>>
>>>
>>> ========================================
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
>>> posting! Please don't post (un)subscribe requests to the list. Use the
>>>  www interface or send it to gmx-users-request at gromacs.org. Can't
>>> post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>>
>>>
>>>
>>
>>
>>
>
> --
> ========================================
>
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
>  Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org. Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
>
>
>





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